Historical rice samples from the 1950s reveal pre-modern-breeding population structure in indica landraces of mainland Southeast Asia

Understanding crop population history requires genetic material that predates modern breeding. In rice (Oryza sativa), extant landraces have revealed a broad regional structure within indica, but the historical depth of these patterns remains uncertain. Here, we analyzed a historical collection of rice landraces assembled in Southeast Asia from 1957 to 1958 (henceforth the Hamada collection). Short-read resequencing yielded 66 high-quality historical samples (seven from North Vietnam, 30 from South Vietnam, 13 from Cambodia, two from Laos, and 14 from Thailand). When integrated with published rice panels, all historical accessions were assigned to indica, and the major regional structure previously described for extant landraces was recovered. Within the Hamada collection, South Vietnamese, Cambodian, and Thai accessions formed a largely continuous mainland Southeast Asian group, whereas North Vietnamese accessions were clearly distinct and comprised two differentiated groups corresponding to two traditional growth seasons (fifth- and tenth-month rice). The fifth-month rice accessions were assigned to the previously reported distinct Vietnam-I5 cluster, showing that this lineage already existed before modern breeding. Admixture graph, f-statistics, and qpWave analyses further indicated that Vietnam-I5 is closely related to a China-associated lineage with a distinct admixture event that cannot be adequately attributed to sampled indica, japonica, or aus groups. Together, these results show that the present-day regional structure of indica was established before modern cultivar replacement, and highlight northern Vietnam as a historical zone of lineage differentiation between Chinese and mainland Southeast Asian rice.